scholarly journals Biphasic Folding Kinetics of RNA Pseudoknots and Telomerase RNA Activity

2007 ◽  
Vol 367 (3) ◽  
pp. 909-924 ◽  
Author(s):  
Song Cao ◽  
Shi-Jie Chen
Keyword(s):  
Telomerase Rna ◽  
Folding Kinetics ◽  
Rna Pseudoknots ◽  
Kinetics Of

scholarly journals Simulation of Folding Kinetics for Aligned RNAs

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 347
Author(s):  
Jiabin Huang ◽  
Björn Voß
Keyword(s):  
Evolutionary Conservation ◽  
Folding Kinetics ◽  
New Approach ◽  
Computational Approaches ◽  
Reasonable Time ◽  
Valuable Method ◽  
Kinetics Of ◽  
Insight Into ◽  
Folding Space ◽  
Standing Problem

Studying the folding kinetics of an RNA can provide insight into its function and is thus a valuable method for RNA analyses. Computational approaches to the simulation of folding kinetics suffer from the exponentially large folding space that needs to be evaluated. Here, we present a new approach that combines structure abstraction with evolutionary conservation to restrict the analysis to common parts of folding spaces of related RNAs. The resulting algorithm can recapitulate the folding kinetics known for single RNAs and is able to analyse even long RNAs in reasonable time. Our program RNAliHiKinetics is the first algorithm for the simulation of consensus folding kinetics and addresses a long-standing problem in a new and unique way.

scholarly journals Modulation of Folding Kinetics of Repeat Proteins: Interplay between Intra- and Interdomain Interactions

2012 ◽  
Vol 103 (7) ◽  
pp. 1555-1565 ◽  
Author(s):  
Tzachi Hagai ◽  
Ariel Azia ◽  
Emmanuel Trizac ◽  
Yaakov Levy
Keyword(s):  
Folding Kinetics ◽  
Repeat Proteins ◽  
Interdomain Interactions ◽  
Kinetics Of

Stability and Folding Kinetics of Structurally Characterized Cytochromec-b562†,‡

Biochemistry ◽  
2006 ◽  
Vol 45 (35) ◽  
pp. 10504-10511 ◽  
Author(s):  
Jasmin Faraone-Mennella ◽  
F. Akif Tezcan ◽  
Harry B. Gray ◽  
Jay R. Winkler
Keyword(s):  
Folding Kinetics ◽  
Kinetics Of

Analysis of the pH-dependent stability and millisecond folding kinetics of horse cytochrome c

2015 ◽  
Vol 585 ◽  
pp. 52-63 ◽  
Author(s):  
Rishu Jain ◽  
Rajesh Kumar ◽  
Sandeep Kumar ◽  
Ritika Chhabra ◽  
Mukesh Chand Agarwal ◽  
...  
Keyword(s):  
Cytochrome C ◽  
Folding Kinetics ◽  
Ph Dependent ◽  
Kinetics Of ◽  
Horse Cytochrome

scholarly journals Ultrafast folding kinetics of WW domains reveal how the amino acid sequence determines the speed limit to protein folding

2019 ◽  
Vol 116 (17) ◽  
pp. 8137-8142 ◽  
Author(s):  
Malwina Szczepaniak ◽  
Manuel Iglesias-Bexiga ◽  
Michele Cerminara ◽  
Mourad Sadqi ◽  
Celia Sanchez de Medina ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Essential Element ◽  
Nanosecond Laser ◽  
Speed Limit ◽  
Free Energy Barrier ◽  
Folding Kinetics ◽  
Folding Rate ◽  
Ww Domains ◽  
Kinetics Of

Protein (un)folding rates depend on the free-energy barrier separating the native and unfolded states and a prefactor term, which sets the timescale for crossing such barrier or folding speed limit. Because extricating these two factors is usually unfeasible, it has been common to assume a constant prefactor and assign all rate variability to the barrier. However, theory and simulations postulate a protein-specific prefactor that contains key mechanistic information. Here, we exploit the special properties of fast-folding proteins to experimentally resolve the folding rate prefactor and investigate how much it varies among structural homologs. We measure the ultrafast (un)folding kinetics of five natural WW domains using nanosecond laser-induced temperature jumps. All five WW domains fold in microseconds, but with a 10-fold difference between fastest and slowest. Interestingly, they all produce biphasic kinetics in which the slower phase corresponds to reequilibration over the small barrier (<3RT) and the faster phase to the downhill relaxation of the minor population residing at the barrier top [transition state ensemble (TSE)]. The fast rate recapitulates the 10-fold range, demonstrating that the folding speed limit of even the simplest all-β fold strongly depends on the amino acid sequence. Given this fold’s simplicity, the most plausible source for such prefactor differences is the presence of nonnative interactions that stabilize the TSE but need to break up before folding resumes. Our results confirm long-standing theoretical predictions and bring into focus the rate prefactor as an essential element for understanding the mechanisms of folding.

scholarly journals Folding Kinetics of Multiple G-Quadruplex Telomeric DNA Structures

2020 ◽  
Vol 118 (3) ◽  
pp. 335a
Author(s):  
Emil L. Kristoffersen ◽  
Andrea Coletta ◽  
Line Lund ◽  
Birgit Schiøtt ◽  
Victoria Birkedal
Keyword(s):  
Folding Kinetics ◽  
Telomeric Dna ◽  
Dna Structures ◽  
G Quadruplex ◽  
Kinetics Of

scholarly journals Folding Kinetics of G-Quadruplexes: Duplex Stem Loops Drive and Accelerate G-Quadruplex Folding

2020 ◽  
Vol 124 (25) ◽  
pp. 5122-5130 ◽  
Author(s):  
Thi Quynh Ngoc Nguyen ◽  
Kah Wai Lim ◽  
Anh Tuân Phan
Keyword(s):  
Folding Kinetics ◽  
G Quadruplex ◽  
Kinetics Of

scholarly journals A comparison of the folding kinetics of a small, artificially selected DNA aptamer with those of equivalently simple naturally occurring proteins

2013 ◽  
Vol 23 (1) ◽  
pp. 56-66 ◽  
Author(s):  
Camille Lawrence ◽  
Alexis Vallée-Bélisle ◽  
Shawn H. Pfeil ◽  
Derek de Mornay ◽  
Everett A. Lipman ◽  
...  
Keyword(s):  
Dna Aptamer ◽  
Folding Kinetics ◽  
Naturally Occurring ◽  
Kinetics Of
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